sequenzo 0.1.17__cp311-cp311-win_amd64.whl → 0.1.19__cp311-cp311-win_amd64.whl

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
  7. sequenzo/clustering/hierarchical_clustering.py +304 -8
  8. sequenzo/define_sequence_data.py +44 -3
  9. sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
  10. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  11. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  12. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  14. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  15. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  16. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  73. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  74. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  75. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
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  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  420. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  421. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  422. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  423. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  424. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  425. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  426. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  427. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  428. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  429. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  430. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  431. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  432. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  433. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  434. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  435. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  436. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  437. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  438. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  439. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  440. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  441. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  442. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  443. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  444. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  445. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  446. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  447. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  448. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  449. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  450. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  451. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  452. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  453. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  454. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  455. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  456. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  457. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  458. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  459. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  460. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  461. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  462. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  463. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  464. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  465. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  466. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  467. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  468. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  469. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  470. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  471. sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
  472. sequenzo-0.1.17.dist-info/RECORD +0 -631
  473. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  474. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  475. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,790 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2012 David Harmon <dharmon@gmail.com>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_ARPACKGENERALIZEDSELFADJOINTEIGENSOLVER_H
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- #define EIGEN_ARPACKGENERALIZEDSELFADJOINTEIGENSOLVER_H
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-
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- #include "../../../../Eigen/Dense"
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-
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- namespace Eigen {
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-
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- namespace internal {
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- template<typename Scalar, typename RealScalar> struct arpack_wrapper;
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- template<typename MatrixSolver, typename MatrixType, typename Scalar, bool BisSPD> struct OP;
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- }
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-
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-
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-
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- template<typename MatrixType, typename MatrixSolver=SimplicialLLT<MatrixType>, bool BisSPD=false>
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- class ArpackGeneralizedSelfAdjointEigenSolver
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- {
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- public:
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- //typedef typename MatrixSolver::MatrixType MatrixType;
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-
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- /** \brief Scalar type for matrices of type \p MatrixType. */
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- typedef typename MatrixType::Scalar Scalar;
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- typedef typename MatrixType::Index Index;
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-
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- /** \brief Real scalar type for \p MatrixType.
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- *
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- * This is just \c Scalar if #Scalar is real (e.g., \c float or
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- * \c Scalar), and the type of the real part of \c Scalar if #Scalar is
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- * complex.
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- */
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- typedef typename NumTraits<Scalar>::Real RealScalar;
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-
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- /** \brief Type for vector of eigenvalues as returned by eigenvalues().
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- *
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- * This is a column vector with entries of type #RealScalar.
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- * The length of the vector is the size of \p nbrEigenvalues.
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- */
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- typedef typename internal::plain_col_type<MatrixType, RealScalar>::type RealVectorType;
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-
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- /** \brief Default constructor.
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- *
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- * The default constructor is for cases in which the user intends to
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- * perform decompositions via compute().
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- *
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- */
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- ArpackGeneralizedSelfAdjointEigenSolver()
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- : m_eivec(),
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- m_eivalues(),
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- m_isInitialized(false),
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- m_eigenvectorsOk(false),
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- m_nbrConverged(0),
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- m_nbrIterations(0)
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- { }
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-
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- /** \brief Constructor; computes generalized eigenvalues of given matrix with respect to another matrix.
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- *
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- * \param[in] A Self-adjoint matrix whose eigenvalues / eigenvectors will
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- * computed. By default, the upper triangular part is used, but can be changed
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- * through the template parameter.
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- * \param[in] B Self-adjoint matrix for the generalized eigenvalue problem.
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- * \param[in] nbrEigenvalues The number of eigenvalues / eigenvectors to compute.
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- * Must be less than the size of the input matrix, or an error is returned.
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- * \param[in] eigs_sigma String containing either "LM", "SM", "LA", or "SA", with
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- * respective meanings to find the largest magnitude , smallest magnitude,
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- * largest algebraic, or smallest algebraic eigenvalues. Alternatively, this
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- * value can contain floating point value in string form, in which case the
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- * eigenvalues closest to this value will be found.
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- * \param[in] options Can be #ComputeEigenvectors (default) or #EigenvaluesOnly.
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- * \param[in] tol What tolerance to find the eigenvalues to. Default is 0, which
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- * means machine precision.
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- *
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- * This constructor calls compute(const MatrixType&, const MatrixType&, Index, string, int, RealScalar)
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- * to compute the eigenvalues of the matrix \p A with respect to \p B. The eigenvectors are computed if
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- * \p options equals #ComputeEigenvectors.
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- *
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- */
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- ArpackGeneralizedSelfAdjointEigenSolver(const MatrixType& A, const MatrixType& B,
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- Index nbrEigenvalues, std::string eigs_sigma="LM",
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- int options=ComputeEigenvectors, RealScalar tol=0.0)
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- : m_eivec(),
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- m_eivalues(),
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- m_isInitialized(false),
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- m_eigenvectorsOk(false),
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- m_nbrConverged(0),
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- m_nbrIterations(0)
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- {
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- compute(A, B, nbrEigenvalues, eigs_sigma, options, tol);
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- }
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-
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- /** \brief Constructor; computes eigenvalues of given matrix.
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- *
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- * \param[in] A Self-adjoint matrix whose eigenvalues / eigenvectors will
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- * computed. By default, the upper triangular part is used, but can be changed
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- * through the template parameter.
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- * \param[in] nbrEigenvalues The number of eigenvalues / eigenvectors to compute.
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- * Must be less than the size of the input matrix, or an error is returned.
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- * \param[in] eigs_sigma String containing either "LM", "SM", "LA", or "SA", with
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- * respective meanings to find the largest magnitude , smallest magnitude,
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- * largest algebraic, or smallest algebraic eigenvalues. Alternatively, this
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- * value can contain floating point value in string form, in which case the
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- * eigenvalues closest to this value will be found.
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- * \param[in] options Can be #ComputeEigenvectors (default) or #EigenvaluesOnly.
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- * \param[in] tol What tolerance to find the eigenvalues to. Default is 0, which
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- * means machine precision.
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- *
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- * This constructor calls compute(const MatrixType&, Index, string, int, RealScalar)
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- * to compute the eigenvalues of the matrix \p A. The eigenvectors are computed if
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- * \p options equals #ComputeEigenvectors.
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- *
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- */
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-
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- ArpackGeneralizedSelfAdjointEigenSolver(const MatrixType& A,
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- Index nbrEigenvalues, std::string eigs_sigma="LM",
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- int options=ComputeEigenvectors, RealScalar tol=0.0)
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- : m_eivec(),
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- m_eivalues(),
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- m_isInitialized(false),
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- m_eigenvectorsOk(false),
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- m_nbrConverged(0),
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- m_nbrIterations(0)
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- {
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- compute(A, nbrEigenvalues, eigs_sigma, options, tol);
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- }
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-
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-
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- /** \brief Computes generalized eigenvalues / eigenvectors of given matrix using the external ARPACK library.
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- *
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- * \param[in] A Selfadjoint matrix whose eigendecomposition is to be computed.
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- * \param[in] B Selfadjoint matrix for generalized eigenvalues.
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- * \param[in] nbrEigenvalues The number of eigenvalues / eigenvectors to compute.
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- * Must be less than the size of the input matrix, or an error is returned.
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- * \param[in] eigs_sigma String containing either "LM", "SM", "LA", or "SA", with
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- * respective meanings to find the largest magnitude , smallest magnitude,
143
- * largest algebraic, or smallest algebraic eigenvalues. Alternatively, this
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- * value can contain floating point value in string form, in which case the
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- * eigenvalues closest to this value will be found.
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- * \param[in] options Can be #ComputeEigenvectors (default) or #EigenvaluesOnly.
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- * \param[in] tol What tolerance to find the eigenvalues to. Default is 0, which
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- * means machine precision.
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- *
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- * \returns Reference to \c *this
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- *
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- * This function computes the generalized eigenvalues of \p A with respect to \p B using ARPACK. The eigenvalues()
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- * function can be used to retrieve them. If \p options equals #ComputeEigenvectors,
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- * then the eigenvectors are also computed and can be retrieved by
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- * calling eigenvectors().
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- *
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- */
158
- ArpackGeneralizedSelfAdjointEigenSolver& compute(const MatrixType& A, const MatrixType& B,
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- Index nbrEigenvalues, std::string eigs_sigma="LM",
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- int options=ComputeEigenvectors, RealScalar tol=0.0);
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-
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- /** \brief Computes eigenvalues / eigenvectors of given matrix using the external ARPACK library.
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- *
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- * \param[in] A Selfadjoint matrix whose eigendecomposition is to be computed.
165
- * \param[in] nbrEigenvalues The number of eigenvalues / eigenvectors to compute.
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- * Must be less than the size of the input matrix, or an error is returned.
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- * \param[in] eigs_sigma String containing either "LM", "SM", "LA", or "SA", with
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- * respective meanings to find the largest magnitude , smallest magnitude,
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- * largest algebraic, or smallest algebraic eigenvalues. Alternatively, this
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- * value can contain floating point value in string form, in which case the
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- * eigenvalues closest to this value will be found.
172
- * \param[in] options Can be #ComputeEigenvectors (default) or #EigenvaluesOnly.
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- * \param[in] tol What tolerance to find the eigenvalues to. Default is 0, which
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- * means machine precision.
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- *
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- * \returns Reference to \c *this
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- *
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- * This function computes the eigenvalues of \p A using ARPACK. The eigenvalues()
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- * function can be used to retrieve them. If \p options equals #ComputeEigenvectors,
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- * then the eigenvectors are also computed and can be retrieved by
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- * calling eigenvectors().
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- *
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- */
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- ArpackGeneralizedSelfAdjointEigenSolver& compute(const MatrixType& A,
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- Index nbrEigenvalues, std::string eigs_sigma="LM",
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- int options=ComputeEigenvectors, RealScalar tol=0.0);
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-
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-
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- /** \brief Returns the eigenvectors of given matrix.
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- *
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- * \returns A const reference to the matrix whose columns are the eigenvectors.
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- *
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- * \pre The eigenvectors have been computed before.
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- *
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- * Column \f$ k \f$ of the returned matrix is an eigenvector corresponding
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- * to eigenvalue number \f$ k \f$ as returned by eigenvalues(). The
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- * eigenvectors are normalized to have (Euclidean) norm equal to one. If
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- * this object was used to solve the eigenproblem for the selfadjoint
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- * matrix \f$ A \f$, then the matrix returned by this function is the
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- * matrix \f$ V \f$ in the eigendecomposition \f$ A V = D V \f$.
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- * For the generalized eigenproblem, the matrix returned is the solution \f$ A V = D B V \f$
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- *
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- * Example: \include SelfAdjointEigenSolver_eigenvectors.cpp
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- * Output: \verbinclude SelfAdjointEigenSolver_eigenvectors.out
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- *
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- * \sa eigenvalues()
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- */
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- const Matrix<Scalar, Dynamic, Dynamic>& eigenvectors() const
209
- {
210
- eigen_assert(m_isInitialized && "ArpackGeneralizedSelfAdjointEigenSolver is not initialized.");
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- eigen_assert(m_eigenvectorsOk && "The eigenvectors have not been computed together with the eigenvalues.");
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- return m_eivec;
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- }
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-
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- /** \brief Returns the eigenvalues of given matrix.
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- *
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- * \returns A const reference to the column vector containing the eigenvalues.
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- *
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- * \pre The eigenvalues have been computed before.
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- *
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- * The eigenvalues are repeated according to their algebraic multiplicity,
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- * so there are as many eigenvalues as rows in the matrix. The eigenvalues
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- * are sorted in increasing order.
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- *
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- * Example: \include SelfAdjointEigenSolver_eigenvalues.cpp
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- * Output: \verbinclude SelfAdjointEigenSolver_eigenvalues.out
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- *
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- * \sa eigenvectors(), MatrixBase::eigenvalues()
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- */
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- const Matrix<Scalar, Dynamic, 1>& eigenvalues() const
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- {
232
- eigen_assert(m_isInitialized && "ArpackGeneralizedSelfAdjointEigenSolver is not initialized.");
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- return m_eivalues;
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- }
235
-
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- /** \brief Computes the positive-definite square root of the matrix.
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- *
238
- * \returns the positive-definite square root of the matrix
239
- *
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- * \pre The eigenvalues and eigenvectors of a positive-definite matrix
241
- * have been computed before.
242
- *
243
- * The square root of a positive-definite matrix \f$ A \f$ is the
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- * positive-definite matrix whose square equals \f$ A \f$. This function
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- * uses the eigendecomposition \f$ A = V D V^{-1} \f$ to compute the
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- * square root as \f$ A^{1/2} = V D^{1/2} V^{-1} \f$.
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- *
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- * Example: \include SelfAdjointEigenSolver_operatorSqrt.cpp
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- * Output: \verbinclude SelfAdjointEigenSolver_operatorSqrt.out
250
- *
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- * \sa operatorInverseSqrt(),
252
- * \ref MatrixFunctions_Module "MatrixFunctions Module"
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- */
254
- Matrix<Scalar, Dynamic, Dynamic> operatorSqrt() const
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- {
256
- eigen_assert(m_isInitialized && "SelfAdjointEigenSolver is not initialized.");
257
- eigen_assert(m_eigenvectorsOk && "The eigenvectors have not been computed together with the eigenvalues.");
258
- return m_eivec * m_eivalues.cwiseSqrt().asDiagonal() * m_eivec.adjoint();
259
- }
260
-
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- /** \brief Computes the inverse square root of the matrix.
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- *
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- * \returns the inverse positive-definite square root of the matrix
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- *
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- * \pre The eigenvalues and eigenvectors of a positive-definite matrix
266
- * have been computed before.
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- *
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- * This function uses the eigendecomposition \f$ A = V D V^{-1} \f$ to
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- * compute the inverse square root as \f$ V D^{-1/2} V^{-1} \f$. This is
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- * cheaper than first computing the square root with operatorSqrt() and
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- * then its inverse with MatrixBase::inverse().
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- *
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- * Example: \include SelfAdjointEigenSolver_operatorInverseSqrt.cpp
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- * Output: \verbinclude SelfAdjointEigenSolver_operatorInverseSqrt.out
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- *
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- * \sa operatorSqrt(), MatrixBase::inverse(),
277
- * \ref MatrixFunctions_Module "MatrixFunctions Module"
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- */
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- Matrix<Scalar, Dynamic, Dynamic> operatorInverseSqrt() const
280
- {
281
- eigen_assert(m_isInitialized && "SelfAdjointEigenSolver is not initialized.");
282
- eigen_assert(m_eigenvectorsOk && "The eigenvectors have not been computed together with the eigenvalues.");
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- return m_eivec * m_eivalues.cwiseInverse().cwiseSqrt().asDiagonal() * m_eivec.adjoint();
284
- }
285
-
286
- /** \brief Reports whether previous computation was successful.
287
- *
288
- * \returns \c Success if computation was successful, \c NoConvergence otherwise.
289
- */
290
- ComputationInfo info() const
291
- {
292
- eigen_assert(m_isInitialized && "ArpackGeneralizedSelfAdjointEigenSolver is not initialized.");
293
- return m_info;
294
- }
295
-
296
- size_t getNbrConvergedEigenValues() const
297
- { return m_nbrConverged; }
298
-
299
- size_t getNbrIterations() const
300
- { return m_nbrIterations; }
301
-
302
- protected:
303
- Matrix<Scalar, Dynamic, Dynamic> m_eivec;
304
- Matrix<Scalar, Dynamic, 1> m_eivalues;
305
- ComputationInfo m_info;
306
- bool m_isInitialized;
307
- bool m_eigenvectorsOk;
308
-
309
- size_t m_nbrConverged;
310
- size_t m_nbrIterations;
311
- };
312
-
313
-
314
-
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-
316
-
317
- template<typename MatrixType, typename MatrixSolver, bool BisSPD>
318
- ArpackGeneralizedSelfAdjointEigenSolver<MatrixType, MatrixSolver, BisSPD>&
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- ArpackGeneralizedSelfAdjointEigenSolver<MatrixType, MatrixSolver, BisSPD>
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- ::compute(const MatrixType& A, Index nbrEigenvalues,
321
- std::string eigs_sigma, int options, RealScalar tol)
322
- {
323
- MatrixType B(0,0);
324
- compute(A, B, nbrEigenvalues, eigs_sigma, options, tol);
325
-
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- return *this;
327
- }
328
-
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-
330
- template<typename MatrixType, typename MatrixSolver, bool BisSPD>
331
- ArpackGeneralizedSelfAdjointEigenSolver<MatrixType, MatrixSolver, BisSPD>&
332
- ArpackGeneralizedSelfAdjointEigenSolver<MatrixType, MatrixSolver, BisSPD>
333
- ::compute(const MatrixType& A, const MatrixType& B, Index nbrEigenvalues,
334
- std::string eigs_sigma, int options, RealScalar tol)
335
- {
336
- eigen_assert(A.cols() == A.rows());
337
- eigen_assert(B.cols() == B.rows());
338
- eigen_assert(B.rows() == 0 || A.cols() == B.rows());
339
- eigen_assert((options &~ (EigVecMask | GenEigMask)) == 0
340
- && (options & EigVecMask) != EigVecMask
341
- && "invalid option parameter");
342
-
343
- bool isBempty = (B.rows() == 0) || (B.cols() == 0);
344
-
345
- // For clarity, all parameters match their ARPACK name
346
- //
347
- // Always 0 on the first call
348
- //
349
- int ido = 0;
350
-
351
- int n = (int)A.cols();
352
-
353
- // User options: "LA", "SA", "SM", "LM", "BE"
354
- //
355
- char whch[3] = "LM";
356
-
357
- // Specifies the shift if iparam[6] = { 3, 4, 5 }, not used if iparam[6] = { 1, 2 }
358
- //
359
- RealScalar sigma = 0.0;
360
-
361
- if (eigs_sigma.length() >= 2 && isalpha(eigs_sigma[0]) && isalpha(eigs_sigma[1]))
362
- {
363
- eigs_sigma[0] = toupper(eigs_sigma[0]);
364
- eigs_sigma[1] = toupper(eigs_sigma[1]);
365
-
366
- // In the following special case we're going to invert the problem, since solving
367
- // for larger magnitude is much much faster
368
- // i.e., if 'SM' is specified, we're going to really use 'LM', the default
369
- //
370
- if (eigs_sigma.substr(0,2) != "SM")
371
- {
372
- whch[0] = eigs_sigma[0];
373
- whch[1] = eigs_sigma[1];
374
- }
375
- }
376
- else
377
- {
378
- eigen_assert(false && "Specifying clustered eigenvalues is not yet supported!");
379
-
380
- // If it's not scalar values, then the user may be explicitly
381
- // specifying the sigma value to cluster the evs around
382
- //
383
- sigma = atof(eigs_sigma.c_str());
384
-
385
- // If atof fails, it returns 0.0, which is a fine default
386
- //
387
- }
388
-
389
- // "I" means normal eigenvalue problem, "G" means generalized
390
- //
391
- char bmat[2] = "I";
392
- if (eigs_sigma.substr(0,2) == "SM" || !(isalpha(eigs_sigma[0]) && isalpha(eigs_sigma[1])) || (!isBempty && !BisSPD))
393
- bmat[0] = 'G';
394
-
395
- // Now we determine the mode to use
396
- //
397
- int mode = (bmat[0] == 'G') + 1;
398
- if (eigs_sigma.substr(0,2) == "SM" || !(isalpha(eigs_sigma[0]) && isalpha(eigs_sigma[1])))
399
- {
400
- // We're going to use shift-and-invert mode, and basically find
401
- // the largest eigenvalues of the inverse operator
402
- //
403
- mode = 3;
404
- }
405
-
406
- // The user-specified number of eigenvalues/vectors to compute
407
- //
408
- int nev = (int)nbrEigenvalues;
409
-
410
- // Allocate space for ARPACK to store the residual
411
- //
412
- Scalar *resid = new Scalar[n];
413
-
414
- // Number of Lanczos vectors, must satisfy nev < ncv <= n
415
- // Note that this indicates that nev != n, and we cannot compute
416
- // all eigenvalues of a mtrix
417
- //
418
- int ncv = std::min(std::max(2*nev, 20), n);
419
-
420
- // The working n x ncv matrix, also store the final eigenvectors (if computed)
421
- //
422
- Scalar *v = new Scalar[n*ncv];
423
- int ldv = n;
424
-
425
- // Working space
426
- //
427
- Scalar *workd = new Scalar[3*n];
428
- int lworkl = ncv*ncv+8*ncv; // Must be at least this length
429
- Scalar *workl = new Scalar[lworkl];
430
-
431
- int *iparam= new int[11];
432
- iparam[0] = 1; // 1 means we let ARPACK perform the shifts, 0 means we'd have to do it
433
- iparam[2] = std::max(300, (int)std::ceil(2*n/std::max(ncv,1)));
434
- iparam[6] = mode; // The mode, 1 is standard ev problem, 2 for generalized ev, 3 for shift-and-invert
435
-
436
- // Used during reverse communicate to notify where arrays start
437
- //
438
- int *ipntr = new int[11];
439
-
440
- // Error codes are returned in here, initial value of 0 indicates a random initial
441
- // residual vector is used, any other values means resid contains the initial residual
442
- // vector, possibly from a previous run
443
- //
444
- int info = 0;
445
-
446
- Scalar scale = 1.0;
447
- //if (!isBempty)
448
- //{
449
- //Scalar scale = B.norm() / std::sqrt(n);
450
- //scale = std::pow(2, std::floor(std::log(scale+1)));
451
- ////M /= scale;
452
- //for (size_t i=0; i<(size_t)B.outerSize(); i++)
453
- // for (typename MatrixType::InnerIterator it(B, i); it; ++it)
454
- // it.valueRef() /= scale;
455
- //}
456
-
457
- MatrixSolver OP;
458
- if (mode == 1 || mode == 2)
459
- {
460
- if (!isBempty)
461
- OP.compute(B);
462
- }
463
- else if (mode == 3)
464
- {
465
- if (sigma == 0.0)
466
- {
467
- OP.compute(A);
468
- }
469
- else
470
- {
471
- // Note: We will never enter here because sigma must be 0.0
472
- //
473
- if (isBempty)
474
- {
475
- MatrixType AminusSigmaB(A);
476
- for (Index i=0; i<A.rows(); ++i)
477
- AminusSigmaB.coeffRef(i,i) -= sigma;
478
-
479
- OP.compute(AminusSigmaB);
480
- }
481
- else
482
- {
483
- MatrixType AminusSigmaB = A - sigma * B;
484
- OP.compute(AminusSigmaB);
485
- }
486
- }
487
- }
488
-
489
- if (!(mode == 1 && isBempty) && !(mode == 2 && isBempty) && OP.info() != Success)
490
- std::cout << "Error factoring matrix" << std::endl;
491
-
492
- do
493
- {
494
- internal::arpack_wrapper<Scalar, RealScalar>::saupd(&ido, bmat, &n, whch, &nev, &tol, resid,
495
- &ncv, v, &ldv, iparam, ipntr, workd, workl,
496
- &lworkl, &info);
497
-
498
- if (ido == -1 || ido == 1)
499
- {
500
- Scalar *in = workd + ipntr[0] - 1;
501
- Scalar *out = workd + ipntr[1] - 1;
502
-
503
- if (ido == 1 && mode != 2)
504
- {
505
- Scalar *out2 = workd + ipntr[2] - 1;
506
- if (isBempty || mode == 1)
507
- Matrix<Scalar, Dynamic, 1>::Map(out2, n) = Matrix<Scalar, Dynamic, 1>::Map(in, n);
508
- else
509
- Matrix<Scalar, Dynamic, 1>::Map(out2, n) = B * Matrix<Scalar, Dynamic, 1>::Map(in, n);
510
-
511
- in = workd + ipntr[2] - 1;
512
- }
513
-
514
- if (mode == 1)
515
- {
516
- if (isBempty)
517
- {
518
- // OP = A
519
- //
520
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = A * Matrix<Scalar, Dynamic, 1>::Map(in, n);
521
- }
522
- else
523
- {
524
- // OP = L^{-1}AL^{-T}
525
- //
526
- internal::OP<MatrixSolver, MatrixType, Scalar, BisSPD>::applyOP(OP, A, n, in, out);
527
- }
528
- }
529
- else if (mode == 2)
530
- {
531
- if (ido == 1)
532
- Matrix<Scalar, Dynamic, 1>::Map(in, n) = A * Matrix<Scalar, Dynamic, 1>::Map(in, n);
533
-
534
- // OP = B^{-1} A
535
- //
536
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = OP.solve(Matrix<Scalar, Dynamic, 1>::Map(in, n));
537
- }
538
- else if (mode == 3)
539
- {
540
- // OP = (A-\sigmaB)B (\sigma could be 0, and B could be I)
541
- // The B * in is already computed and stored at in if ido == 1
542
- //
543
- if (ido == 1 || isBempty)
544
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = OP.solve(Matrix<Scalar, Dynamic, 1>::Map(in, n));
545
- else
546
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = OP.solve(B * Matrix<Scalar, Dynamic, 1>::Map(in, n));
547
- }
548
- }
549
- else if (ido == 2)
550
- {
551
- Scalar *in = workd + ipntr[0] - 1;
552
- Scalar *out = workd + ipntr[1] - 1;
553
-
554
- if (isBempty || mode == 1)
555
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = Matrix<Scalar, Dynamic, 1>::Map(in, n);
556
- else
557
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = B * Matrix<Scalar, Dynamic, 1>::Map(in, n);
558
- }
559
- } while (ido != 99);
560
-
561
- if (info == 1)
562
- m_info = NoConvergence;
563
- else if (info == 3)
564
- m_info = NumericalIssue;
565
- else if (info < 0)
566
- m_info = InvalidInput;
567
- else if (info != 0)
568
- eigen_assert(false && "Unknown ARPACK return value!");
569
- else
570
- {
571
- // Do we compute eigenvectors or not?
572
- //
573
- int rvec = (options & ComputeEigenvectors) == ComputeEigenvectors;
574
-
575
- // "A" means "All", use "S" to choose specific eigenvalues (not yet supported in ARPACK))
576
- //
577
- char howmny[2] = "A";
578
-
579
- // if howmny == "S", specifies the eigenvalues to compute (not implemented in ARPACK)
580
- //
581
- int *select = new int[ncv];
582
-
583
- // Final eigenvalues
584
- //
585
- m_eivalues.resize(nev, 1);
586
-
587
- internal::arpack_wrapper<Scalar, RealScalar>::seupd(&rvec, howmny, select, m_eivalues.data(), v, &ldv,
588
- &sigma, bmat, &n, whch, &nev, &tol, resid, &ncv,
589
- v, &ldv, iparam, ipntr, workd, workl, &lworkl, &info);
590
-
591
- if (info == -14)
592
- m_info = NoConvergence;
593
- else if (info != 0)
594
- m_info = InvalidInput;
595
- else
596
- {
597
- if (rvec)
598
- {
599
- m_eivec.resize(A.rows(), nev);
600
- for (int i=0; i<nev; i++)
601
- for (int j=0; j<n; j++)
602
- m_eivec(j,i) = v[i*n+j] / scale;
603
-
604
- if (mode == 1 && !isBempty && BisSPD)
605
- internal::OP<MatrixSolver, MatrixType, Scalar, BisSPD>::project(OP, n, nev, m_eivec.data());
606
-
607
- m_eigenvectorsOk = true;
608
- }
609
-
610
- m_nbrIterations = iparam[2];
611
- m_nbrConverged = iparam[4];
612
-
613
- m_info = Success;
614
- }
615
-
616
- delete[] select;
617
- }
618
-
619
- delete[] v;
620
- delete[] iparam;
621
- delete[] ipntr;
622
- delete[] workd;
623
- delete[] workl;
624
- delete[] resid;
625
-
626
- m_isInitialized = true;
627
-
628
- return *this;
629
- }
630
-
631
-
632
- // Single precision
633
- //
634
- extern "C" void ssaupd_(int *ido, char *bmat, int *n, char *which,
635
- int *nev, float *tol, float *resid, int *ncv,
636
- float *v, int *ldv, int *iparam, int *ipntr,
637
- float *workd, float *workl, int *lworkl,
638
- int *info);
639
-
640
- extern "C" void sseupd_(int *rvec, char *All, int *select, float *d,
641
- float *z, int *ldz, float *sigma,
642
- char *bmat, int *n, char *which, int *nev,
643
- float *tol, float *resid, int *ncv, float *v,
644
- int *ldv, int *iparam, int *ipntr, float *workd,
645
- float *workl, int *lworkl, int *ierr);
646
-
647
- // Double precision
648
- //
649
- extern "C" void dsaupd_(int *ido, char *bmat, int *n, char *which,
650
- int *nev, double *tol, double *resid, int *ncv,
651
- double *v, int *ldv, int *iparam, int *ipntr,
652
- double *workd, double *workl, int *lworkl,
653
- int *info);
654
-
655
- extern "C" void dseupd_(int *rvec, char *All, int *select, double *d,
656
- double *z, int *ldz, double *sigma,
657
- char *bmat, int *n, char *which, int *nev,
658
- double *tol, double *resid, int *ncv, double *v,
659
- int *ldv, int *iparam, int *ipntr, double *workd,
660
- double *workl, int *lworkl, int *ierr);
661
-
662
-
663
- namespace internal {
664
-
665
- template<typename Scalar, typename RealScalar> struct arpack_wrapper
666
- {
667
- static inline void saupd(int *ido, char *bmat, int *n, char *which,
668
- int *nev, RealScalar *tol, Scalar *resid, int *ncv,
669
- Scalar *v, int *ldv, int *iparam, int *ipntr,
670
- Scalar *workd, Scalar *workl, int *lworkl, int *info)
671
- {
672
- EIGEN_STATIC_ASSERT(!NumTraits<Scalar>::IsComplex, NUMERIC_TYPE_MUST_BE_REAL)
673
- }
674
-
675
- static inline void seupd(int *rvec, char *All, int *select, Scalar *d,
676
- Scalar *z, int *ldz, RealScalar *sigma,
677
- char *bmat, int *n, char *which, int *nev,
678
- RealScalar *tol, Scalar *resid, int *ncv, Scalar *v,
679
- int *ldv, int *iparam, int *ipntr, Scalar *workd,
680
- Scalar *workl, int *lworkl, int *ierr)
681
- {
682
- EIGEN_STATIC_ASSERT(!NumTraits<Scalar>::IsComplex, NUMERIC_TYPE_MUST_BE_REAL)
683
- }
684
- };
685
-
686
- template <> struct arpack_wrapper<float, float>
687
- {
688
- static inline void saupd(int *ido, char *bmat, int *n, char *which,
689
- int *nev, float *tol, float *resid, int *ncv,
690
- float *v, int *ldv, int *iparam, int *ipntr,
691
- float *workd, float *workl, int *lworkl, int *info)
692
- {
693
- ssaupd_(ido, bmat, n, which, nev, tol, resid, ncv, v, ldv, iparam, ipntr, workd, workl, lworkl, info);
694
- }
695
-
696
- static inline void seupd(int *rvec, char *All, int *select, float *d,
697
- float *z, int *ldz, float *sigma,
698
- char *bmat, int *n, char *which, int *nev,
699
- float *tol, float *resid, int *ncv, float *v,
700
- int *ldv, int *iparam, int *ipntr, float *workd,
701
- float *workl, int *lworkl, int *ierr)
702
- {
703
- sseupd_(rvec, All, select, d, z, ldz, sigma, bmat, n, which, nev, tol, resid, ncv, v, ldv, iparam, ipntr,
704
- workd, workl, lworkl, ierr);
705
- }
706
- };
707
-
708
- template <> struct arpack_wrapper<double, double>
709
- {
710
- static inline void saupd(int *ido, char *bmat, int *n, char *which,
711
- int *nev, double *tol, double *resid, int *ncv,
712
- double *v, int *ldv, int *iparam, int *ipntr,
713
- double *workd, double *workl, int *lworkl, int *info)
714
- {
715
- dsaupd_(ido, bmat, n, which, nev, tol, resid, ncv, v, ldv, iparam, ipntr, workd, workl, lworkl, info);
716
- }
717
-
718
- static inline void seupd(int *rvec, char *All, int *select, double *d,
719
- double *z, int *ldz, double *sigma,
720
- char *bmat, int *n, char *which, int *nev,
721
- double *tol, double *resid, int *ncv, double *v,
722
- int *ldv, int *iparam, int *ipntr, double *workd,
723
- double *workl, int *lworkl, int *ierr)
724
- {
725
- dseupd_(rvec, All, select, d, v, ldv, sigma, bmat, n, which, nev, tol, resid, ncv, v, ldv, iparam, ipntr,
726
- workd, workl, lworkl, ierr);
727
- }
728
- };
729
-
730
-
731
- template<typename MatrixSolver, typename MatrixType, typename Scalar, bool BisSPD>
732
- struct OP
733
- {
734
- static inline void applyOP(MatrixSolver &OP, const MatrixType &A, int n, Scalar *in, Scalar *out);
735
- static inline void project(MatrixSolver &OP, int n, int k, Scalar *vecs);
736
- };
737
-
738
- template<typename MatrixSolver, typename MatrixType, typename Scalar>
739
- struct OP<MatrixSolver, MatrixType, Scalar, true>
740
- {
741
- static inline void applyOP(MatrixSolver &OP, const MatrixType &A, int n, Scalar *in, Scalar *out)
742
- {
743
- // OP = L^{-1} A L^{-T} (B = LL^T)
744
- //
745
- // First solve L^T out = in
746
- //
747
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = OP.matrixU().solve(Matrix<Scalar, Dynamic, 1>::Map(in, n));
748
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = OP.permutationPinv() * Matrix<Scalar, Dynamic, 1>::Map(out, n);
749
-
750
- // Then compute out = A out
751
- //
752
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = A * Matrix<Scalar, Dynamic, 1>::Map(out, n);
753
-
754
- // Then solve L out = out
755
- //
756
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = OP.permutationP() * Matrix<Scalar, Dynamic, 1>::Map(out, n);
757
- Matrix<Scalar, Dynamic, 1>::Map(out, n) = OP.matrixL().solve(Matrix<Scalar, Dynamic, 1>::Map(out, n));
758
- }
759
-
760
- static inline void project(MatrixSolver &OP, int n, int k, Scalar *vecs)
761
- {
762
- // Solve L^T out = in
763
- //
764
- Matrix<Scalar, Dynamic, Dynamic>::Map(vecs, n, k) = OP.matrixU().solve(Matrix<Scalar, Dynamic, Dynamic>::Map(vecs, n, k));
765
- Matrix<Scalar, Dynamic, Dynamic>::Map(vecs, n, k) = OP.permutationPinv() * Matrix<Scalar, Dynamic, Dynamic>::Map(vecs, n, k);
766
- }
767
-
768
- };
769
-
770
- template<typename MatrixSolver, typename MatrixType, typename Scalar>
771
- struct OP<MatrixSolver, MatrixType, Scalar, false>
772
- {
773
- static inline void applyOP(MatrixSolver &OP, const MatrixType &A, int n, Scalar *in, Scalar *out)
774
- {
775
- eigen_assert(false && "Should never be in here...");
776
- }
777
-
778
- static inline void project(MatrixSolver &OP, int n, int k, Scalar *vecs)
779
- {
780
- eigen_assert(false && "Should never be in here...");
781
- }
782
-
783
- };
784
-
785
- } // end namespace internal
786
-
787
- } // end namespace Eigen
788
-
789
- #endif // EIGEN_ARPACKSELFADJOINTEIGENSOLVER_H
790
-